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- PDB-3pzh: Crystal structure of maize CK2 alpha in complex with emodin at 1.... -

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Basic information

Entry
Database: PDB / ID: 3pzh
TitleCrystal structure of maize CK2 alpha in complex with emodin at 1.92 A resolution
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / protein kinase / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


regulation of transcription by RNA polymerase I / regulation of transcription by RNA polymerase III / protein kinase CK2 complex / non-specific serine/threonine protein kinase / regulation of cell cycle / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / ATP binding ...regulation of transcription by RNA polymerase I / regulation of transcription by RNA polymerase III / protein kinase CK2 complex / non-specific serine/threonine protein kinase / regulation of cell cycle / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / ATP binding / nucleus / cytosol
Similarity search - Function
Casein Kinase 2, subunit alpha / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site ...Casein Kinase 2, subunit alpha / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / 3-METHYL-1,6,8-TRIHYDROXYANTHRAQUINONE / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Rigid Body / Resolution: 1.919 Å
AuthorsBattistutta, R. / Mazzorana, M.
CitationJournal: to be published
Title: Structural and functional analysis of the flexible regions of the catalytic alpha-subunit of protein kinase CK2
Authors: Papinutto, E. / Ranchio, A. / Lolli, G. / Pinna, L.A. / Battistutta, R.
History
DepositionDec 14, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,28813
Polymers39,3671
Non-polymers92012
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)142.629, 59.376, 44.860
Angle α, β, γ (deg.)90.000, 103.060, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-417-

HOH

21A-485-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Casein kinase II subunit alpha / CK II / CK2-alpha


Mass: 39367.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: ACK2 / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli)
References: UniProt: P28523, non-specific serine/threonine protein kinase

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Non-polymers , 5 types, 262 molecules

#2: Chemical ChemComp-EMO / 3-METHYL-1,6,8-TRIHYDROXYANTHRAQUINONE / EMODIN


Mass: 270.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H10O5
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.66 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% PEG 4000, 0.2M sodium acetate, 0.1M TrisHCl, pH 8, vapor diffusion, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 12, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.919→69.471 Å / Num. all: 26706 / Num. obs: 26706 / % possible obs: 95.4 % / Redundancy: 2.5 % / Biso Wilson estimate: 17.79 Å2 / Rsym value: 0.057 / Net I/σ(I): 13.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.92-2.022.10.4680.3652.1712234710.2890.4680.3652.486
2.02-2.142.60.3320.2642.3968137870.1980.3320.264498
2.14-2.292.50.2290.1824.3889034950.1380.2290.1825.797
2.29-2.482.60.150.126.5861633380.090.150.128.198.1
2.48-2.712.60.1140.0918.4782530280.0680.1140.09110.497.7
2.71-3.032.60.0710.05713.4711827340.0420.0710.05715.797.3
3.03-3.52.60.0450.03620.3634224270.0260.0450.03623.896.7
3.5-4.292.60.030.02428.7524220100.0180.030.02434.895.8
4.29-6.072.60.0270.02228.3412915620.0160.0270.02238.894.9
6.07-41.4512.60.0250.0230.422138540.0150.0250.0241.792.4

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
ProDCdata collection
XSCALEdata scaling
RefinementMethod to determine structure: Rigid Body / Resolution: 1.919→36.518 Å / Occupancy max: 1 / Occupancy min: 0.32 / FOM work R set: 0.8649 / SU ML: 0.23 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2086 1248 4.98 %Random
Rwork0.1586 ---
obs0.1611 25068 89.21 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.105 Å2 / ksol: 0.369 e/Å3
Displacement parametersBiso max: 96.81 Å2 / Biso mean: 26.64 Å2 / Biso min: 5.39 Å2
Baniso -1Baniso -2Baniso -3
1--3.9223 Å20 Å2-1.6829 Å2
2--10.5091 Å20 Å2
3----6.5869 Å2
Refinement stepCycle: LAST / Resolution: 1.919→36.518 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2742 0 61 250 3053
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072874
X-RAY DIFFRACTIONf_angle_d1.0133870
X-RAY DIFFRACTIONf_chiral_restr0.071402
X-RAY DIFFRACTIONf_plane_restr0.004491
X-RAY DIFFRACTIONf_dihedral_angle_d13.661086
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9187-1.99550.3152820.24222016209868
1.9955-2.08640.2741340.19772504263885
2.0864-2.19630.20681370.16892619275688
2.1963-2.33390.25861330.17152635276890
2.3339-2.51410.21321360.15922761289793
2.5141-2.7670.24321480.16052821296995
2.767-3.16720.19791720.15632798297095
3.1672-3.98960.20571430.14242847299095
3.9896-36.52510.1621630.1422819298293
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.72080.25580.30730.54930.16750.4773-0.07850.07770.1726-0.0076-0.01240.0056-0.14090.14810.0530.1012-0.05490.00510.0741-0.01390.111627.251910.99579.8421
20.91030.23580.5980.10920.06320.4747-0.0086-0.15310.0331-0.0098-0.0050.0118-0.0217-0.0060.00540.06830.00330.01310.0761-0.02180.067415.8199-1.82739.9067
30.5429-0.2216-0.14740.13310.06890.2101-0.0161-0.2329-0.08160.06130.0456-0.00960.03540.0925-0.01340.08090.036-0.02330.13910.01790.086612.6171-12.284317.5752
40.6075-0.10640.17450.040.10810.7720.22880.041-0.6031-0.16660.07120.0020.46460.1707-0.2160.28220.0463-0.07440.1406-0.05770.228317.4876-22.6233.5348
50.24790.05220.38610.02190.08940.94590.30810.0324-0.21350.06540.0837-0.11880.48710.0516-0.27090.3707-0.0046-0.06340.1985-0.01860.409615.1916-26.67098.8941
60.7185-0.21790.33810.3929-0.10690.23090.021-0.3051-0.1329-0.03190.14520.1419-0.0051-0.0468-0.11590.0781-0.002-0.00370.17430.03280.08581.8131-7.3479.8975
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND RESID 7:118)A7 - 118
2X-RAY DIFFRACTION2(CHAIN A AND RESID 119:216)A119 - 216
3X-RAY DIFFRACTION3(CHAIN A AND RESID 217:237)A217 - 237
4X-RAY DIFFRACTION4(CHAIN A AND RESID 238:265)A238 - 265
5X-RAY DIFFRACTION5(CHAIN A AND RESID 266:282)A266 - 282
6X-RAY DIFFRACTION6(CHAIN A AND RESID 283:334)A283 - 334

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